Summary of Study ST001830

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001156. The data can be accessed directly via it's Project DOI: 10.21228/M88T3S This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001830
Study TitleExhaustive analysis of endogenous oxPCs in APAP-treated mice.
Study SummaryA single dose of APAP at 300 mg/kg body weight was intraperitoneally administered into eight-week-old C57BL/6J male mice. After extraction of hepatic lipids, oxPCs were analyzed by LC/HRMS/MS. All mass spectrometry raw data obtained in this study were deposited.
Institute
Kyushu university
Last NameMatsuoka
First NameYuta
Address3-1-1 Maidashi Higashi-ku, Fukuoka, Not USCanada, 812-8582, Japan
Emailymatsu1205@gmail.com
Phone+81-92-642-6624
Submit Date2021-06-13
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2021-10-14
Release Version1
Yuta Matsuoka Yuta Matsuoka
https://dx.doi.org/10.21228/M88T3S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001156
Project DOI:doi: 10.21228/M88T3S
Project Title:Structural Library and Visualization of Endogenously Oxidized Phosphatidylcholines Using Mass Spectrometry-based Techniques
Project Summary:Although oxidized phosphatidylcholines (oxPCs) play critical roles in numerous pathological events, the type and production site(s) of endogenous oxPCs remain unknown because of the lack of related structural information and analytical methods. Herein, a library of 465 oxPCs was constructed using high-resolution mass spectrometry (HRMS)-based analytical methods and employed to detect 70 oxPCs in mice with acetaminophen-induced acute liver failure.
Institute:Kyushu university
Last Name:Matsuoka
First Name:Yuta
Address:3-1-1 Maidashi Higashi-ku
Email:ymatsu1205@gmail.com
Phone:+81-92-642-6624

Subject:

Subject ID:SU001907
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Treatments Treatment times Air conditions
SA170005S2_0194C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170006S2_0193C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170007S2_0192C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170008S2_0195C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170009S2_0198C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170010S2_0200C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170011S2_0199C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170012S2_0191C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170013S2_0196C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170014S2_0189C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170015S2_0184C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170016S2_0183C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170017S2_0182C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170018S2_0185C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170019S2_0186C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170020S2_0201C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170021S2_0188C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170022S2_0187C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170023S2_0190C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170024S2_0197C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170025S2_0202C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170026S2_0204C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170027S2_0205C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170028S2_0203C57BL6J, APAP 300 mg/kg+MT 20 mg/kg 4h normal air
SA170029S2_0160C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170030S2_0159C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170031S2_0161C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170032S2_0168C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170033S2_0158C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170034S2_0162C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170035S2_0181C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170036S2_0178C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170037S2_0177C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170038S2_0179C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170039S2_0180C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170040S2_0169C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170041S2_0157C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170042S2_0171C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170043S2_0173C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170044S2_0174C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170045S2_0175C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170046S2_0176C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170047S2_0170C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170048S2_0163C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170049S2_0172C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170050S2_0164C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170051S2_0167C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170052S2_0166C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170053S2_0165C57BL6J, APAP 300 mg/kg+NAC 300 mg/kg 4h normal air
SA170054S2_0054C57BL6J, APAP 300 mg/kg 1h normal air
SA170055S2_0053C57BL6J, APAP 300 mg/kg 1h normal air
SA170056S2_0050C57BL6J, APAP 300 mg/kg 1h normal air
SA170057S2_0036C57BL6J, APAP 300 mg/kg 1h normal air
SA170058S2_0038C57BL6J, APAP 300 mg/kg 1h normal air
SA170059S2_0039C57BL6J, APAP 300 mg/kg 1h normal air
SA170060S2_0040C57BL6J, APAP 300 mg/kg 1h normal air
SA170061S2_0052C57BL6J, APAP 300 mg/kg 1h normal air
SA170062S2_0035C57BL6J, APAP 300 mg/kg 1h normal air
SA170063S2_0031C57BL6J, APAP 300 mg/kg 1h normal air
SA170064S2_0032C57BL6J, APAP 300 mg/kg 1h normal air
SA170065S2_0033C57BL6J, APAP 300 mg/kg 1h normal air
SA170066S2_0034C57BL6J, APAP 300 mg/kg 1h normal air
SA170067S2_0041C57BL6J, APAP 300 mg/kg 1h normal air
SA170068S2_0037C57BL6J, APAP 300 mg/kg 1h normal air
SA170069S2_0047C57BL6J, APAP 300 mg/kg 1h normal air
SA170070S2_0051C57BL6J, APAP 300 mg/kg 1h normal air
SA170071S2_0042C57BL6J, APAP 300 mg/kg 1h normal air
SA170072S2_0045C57BL6J, APAP 300 mg/kg 1h normal air
SA170073S2_0046C57BL6J, APAP 300 mg/kg 1h normal air
SA170074S2_0043C57BL6J, APAP 300 mg/kg 1h normal air
SA170075S2_0044C57BL6J, APAP 300 mg/kg 1h normal air
SA170076S2_0048C57BL6J, APAP 300 mg/kg 1h normal air
SA170077S2_0049C57BL6J, APAP 300 mg/kg 1h normal air
SA170078S2_0155C57BL6J, APAP 300 mg/kg 24h normal air
SA170079S2_0137C57BL6J, APAP 300 mg/kg 24h normal air
SA170080S2_0156C57BL6J, APAP 300 mg/kg 24h normal air
SA170081S2_0147C57BL6J, APAP 300 mg/kg 24h normal air
SA170082S2_0153C57BL6J, APAP 300 mg/kg 24h normal air
SA170083S2_0136C57BL6J, APAP 300 mg/kg 24h normal air
SA170084S2_0148C57BL6J, APAP 300 mg/kg 24h normal air
SA170085S2_0149C57BL6J, APAP 300 mg/kg 24h normal air
SA170086S2_0150C57BL6J, APAP 300 mg/kg 24h normal air
SA170087S2_0152C57BL6J, APAP 300 mg/kg 24h normal air
SA170088S2_0151C57BL6J, APAP 300 mg/kg 24h normal air
SA170089S2_0154C57BL6J, APAP 300 mg/kg 24h normal air
SA170090S2_0144C57BL6J, APAP 300 mg/kg 24h normal air
SA170091S2_0140C57BL6J, APAP 300 mg/kg 24h normal air
SA170092S2_0141C57BL6J, APAP 300 mg/kg 24h normal air
SA170093S2_0139C57BL6J, APAP 300 mg/kg 24h normal air
SA170094S2_0138C57BL6J, APAP 300 mg/kg 24h normal air
SA170095S2_0146C57BL6J, APAP 300 mg/kg 24h normal air
SA170096S2_0142C57BL6J, APAP 300 mg/kg 24h normal air
SA170097S2_0143C57BL6J, APAP 300 mg/kg 24h normal air
SA170098S2_0134C57BL6J, APAP 300 mg/kg 24h normal air
SA170099S2_0135C57BL6J, APAP 300 mg/kg 24h normal air
SA170100S2_0133C57BL6J, APAP 300 mg/kg 24h normal air
SA170101S2_0145C57BL6J, APAP 300 mg/kg 24h normal air
SA170102S2_0231C57BL6J, APAP 300 mg/kg 2h 18O2 air
SA170103S2_0232C57BL6J, APAP 300 mg/kg 2h 18O2 air
SA170104S2_0069C57BL6J, APAP 300 mg/kg 2h normal air
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 232

Collection:

Collection ID:CO001900
Collection Summary:The animals were anesthetized with a solution of hydrochloric acid medetomidine (Kyoritsu Seiyaku Corporation, Tokyo, Japan), midazolam (Sandoz K.K., Tokyo, Japan), and butorphanol (Meiji Seika Pharma Co., Ltd., Tokyo, Japan) 1, 2, 4, 8, or 24 h after APAP administration. Mouse liver samples were collected, and the liver samples were immediately frozen in liquid nitrogen.
Sample Type:Liver

Treatment:

Treatment ID:TR001920
Treatment Summary:A single dose of APAP at 300 mg/kg body weight was intraperitoneally administered into eight-week-old C57BL/6J male mice. To suppress LPO induction by APAP administration, either 300 mg/kg body weight of NAC or 20 mg/kg body weight of MT in saline was intraperitoneally injected 1 h after APAP administration.

Sample Preparation:

Sampleprep ID:SP001913
Sampleprep Summary:Hepatic lipids were extracted from the liver samples according to the modified Bligh and Dyer method. Briefly, 1 mL of extraction solution (methanol:chloroform:water = 5:2:2) containing 100 μM dibutylhydroxytoluene, 100 μM ethylenediaminetetraacetic acid, and 100 nM PC15:0/18:1-d7 was added to a frozen tissue sample (wet weight: approx. 50 mg), and then, the sample was homogenized using a Macro Smash homogenizer. Subsequently, the extraction solutions were sonicated on ice bath for 5 min. After centrifugation (6,000 g, 10 min, 4°C), 700 µL of the supernatant was collected, and then, 235 µL chloroform and 155 µL water were added to the supernatant. The organic layer was collected in a glass tube and dried under a stream of nitrogen gas; the dried residue was dissolved in methanol (200 µL) and stored at −80 °C before performing the LC/HRMS/MS experiments.

Combined analysis:

Analysis ID AN002970 AN002971
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Nexera LC system (Shimadzu Co., Kyoto, Japan) Nexera LC system (Shimadzu Co., Kyoto, Japan)
Column Inertsil ODS-P (150 x 2.1mm,3um) Inertsil ODS-P (150 x 2.1mm,3um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Normalized amount Normalized amount

Chromatography:

Chromatography ID:CH002200
Instrument Name:Nexera LC system (Shimadzu Co., Kyoto, Japan)
Column Name:Inertsil ODS-P (150 x 2.1mm,3um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002760
Analysis ID:AN002970
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Individual oxPCs were identified by full-scan MS/data-dependent MS/MS or parallel reaction monitoring (PRM). The ionization conditions were as follows: ionization mode = positive, sheath gas flow rate = 40 arbitrary units, auxiliary gas flow rate = 10 arbitrary units, spray voltage = 2000 V, capillary temperature = 265 °C, S-lens level = 50, and heater temperature = 425 °C. The experimental conditions for full-scan MS were as follows: resolving power = 70000, automatic gain control target = 1 × 106, trap fill time = 100 ms, scan range = m/z 120–1500. The experimental conditions for MS/MS and PRM were as follows: resolving power = 17500, automatic gain control target = 1 × 106, trap fill time = 80 ms, isolation width = ±0.6 Da, fixed first mass = m/z 80, normalized collision energy = 20 or 35 eV, intensity threshold of precursor ions for MS/MS analysis = 3100, apex trigger = 2–4 s, and dynamic exclusion = 2 s. The intensity threshold of precursor ions for MS/MS analysis and the dynamic exclusion were set to 1 × 104 and 1 s, respectively. The inclusion list contained 465 precursor ions (m/z) of oxPCs for MS/MS analysis. LC/HRMS/MS analysis was controlled using Xcalibur 4.2.47 software (Thermo Fisher Scientific).
Ion Mode:POSITIVE
  
MS ID:MS002761
Analysis ID:AN002971
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Individual oxPCs were identified by full-scan MS/data-dependent MS/MS or parallel reaction monitoring (PRM). The ionization conditions were as follows: ionization mode = negative, sheath gas flow rate = 40 arbitrary units, auxiliary gas flow rate = 10 arbitrary units, spray voltage = 2000 V, capillary temperature = 265 °C, S-lens level = 50, and heater temperature = 425 °C. The experimental conditions for full-scan MS were as follows: resolving power = 70000, automatic gain control target = 1 × 106, trap fill time = 100 ms, scan range = m/z 120–1500. The experimental conditions for MS/MS and PRM were as follows: resolving power = 17500, automatic gain control target = 1 × 106, trap fill time = 80 ms, isolation width = ±0.6 Da, fixed first mass = m/z 80, normalized collision energy = 20 or 35 eV, intensity threshold of precursor ions for MS/MS analysis = 3100, apex trigger = 2–4 s, and dynamic exclusion = 2 s. The intensity threshold of precursor ions for MS/MS analysis and the dynamic exclusion were set to 1 × 104 and 1 s, respectively. The inclusion list contained 465 precursor ions (m/z) of oxPCs for MS/MS analysis. LC/HRMS/MS analysis was controlled using Xcalibur 4.2.47 software (Thermo Fisher Scientific).
Ion Mode:NEGATIVE
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